New Tricks with Old Dogs: Computational Identification and Experimental Validation of New miRNA–mRNA Regulation in hiPSC-CMs

Abstract

Cardiovascular disease is still the leading cause of morbidity and mortality worldwide. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have become a valuable widespread in vitro model to study cardiac disease. Herein, we employ the hiPSC-CM model to identify novel miRNA–mRNA interaction partners during cardiac differentiation and β-adrenergic stress. Whole transcriptome and small RNA sequencing data were combined to identify novel miRNA–mRNA interactions. Briefly, mRNA and miRNA expression profiles were integrated with miRNA target predictions to identify significant statistical dependencies between a miRNA and its candidate target set. We show by experimental validation that our approach discriminates true from false miRNA target predictions. Thereby, we identified several differentially expressed miRNAs and focused on the two top candidates: miR-99a-5p in the context of cardiac differentiation and miR-212-3p in the context of β-adrenergic stress. We validated some target mRNA candidates by 3′ UTR luciferase assays as well as in transfection experiments in the hiPSC-CM model system. Our data show that iPSC-derived cardiomyocytes and computational modeling can be used to uncover new valid miRNA–mRNA interactions beyond current knowledge.

Expression of Extracellular Vesicle PIWI-Interacting RNAs Throughout hiPSC-Cardiomyocyte Differentiation

“…Several types of short ncRNA were found to be particularly enriched in these vesicles, including miRNA, tRNA, piRNA, and snoRNA. Numerous studies have highlighted the role of ncRNA in the heart ( Bian et al, 2021 ; Martyniak et al, 2021 ; Bencun et al, 2022 ), in parallel with the growing evidence on EV as key players in cardiac diseases and heart regeneration ( Adamiak and Sahoo, 2018 ; Santoso et al, 2020 ; Lima Correa et al, 2021 ).…”

mRNA Metabolism in Health and Disease

“…miRNAs have the capability of regulating gene expression at the post-transcriptional level either by inhibiting mRNA translation or by promoting mRNA degradation. In the manuscript of Bencun and colleagues [ 16 ], authors used whole transcriptome and small RNA sequencing data from human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to identify novel miRNA–mRNA interactions during cardiac differentiation and β-adrenergic stress. Experimental validation of novel miRNA-mRNA interactions allowed authors to highlight hiPSC-CMs as a useful model to study cardiac miRNA–mRNA interactions.…”